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http://huttenhower.sph.harvard.edu/galaxy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: LEfSe (RRID:SCR_014609) Copy
https://www.thermofisher.com/order/catalog/product/4363991
Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.
Proper citation: Primer Express (RRID:SCR_014326) Copy
https://edspace.american.edu/openbehavior/
Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.
Proper citation: OpenBehavior (RRID:SCR_015938) Copy
https://CRAN.R-project.org/package=Boruta
Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).
Proper citation: Boruta (RRID:SCR_016234) Copy
http://www.hkl-xray.com/hkl-2000
Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.
Proper citation: HKL-2000 (RRID:SCR_015547) Copy
https://github.com/vinguyenle/k-FLBPCM-method
Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.
Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy
Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.
Proper citation: Berkeley Drosophila Genome Project (RRID:SCR_013094) Copy
Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.
Proper citation: EZ-C1 FreeViewer (RRID:SCR_014277) Copy
Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples.
Proper citation: Cellosaurus (RRID:SCR_013869) Copy
A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions.
Proper citation: machine learning open source software (RRID:SCR_013990) Copy
http://www.cancer.gov/researchandfunding
Federal government agency for cancer research and training established in 1937. National Cancer Program is responsibility of NCI to coordinate, conduct and support research, training, health information dissemination with respect to cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and continuing care of cancer patients and families of cancer patients. Supports construction of laboratories, clinics, and related facilities necessary for cancer research through award of grants.
Proper citation: National Cancer Institute (RRID:SCR_011176) Copy
https://github.com/ChristophRau/wMICA
Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.
Proper citation: wMICA (RRID:SCR_015490) Copy
http://www.dbemt.bioinfo-minzhao.org/
Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.
Proper citation: dbEMT 2 (RRID:SCR_024692) Copy
https://github.com/yhoogstrate/dr-disco
Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.
Proper citation: Dr. Disco (RRID:SCR_021739) Copy
http://carbonyldb.missouri.edu/CarbonylDB/index.php/
Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.
Proper citation: CarbonylDB (RRID:SCR_023924) Copy
https://github.com/olivierfriard/BORIS
Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.
Proper citation: Behavioral Observation Research Interactive Software (RRID:SCR_021509) Copy
https://github.com/ZhenjiangFan/DAG-deepVASE
Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.
Proper citation: DAG-deepVASE (RRID:SCR_023612) Copy
https://github.com/lapphe/raspberry_rat
Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.
Proper citation: Rasberry rat (RRID:SCR_023467) Copy
http://www.cma.mgh.harvard.edu/
A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes.
Proper citation: MGH Center for Morphometric Analysis (RRID:SCR_000885) Copy
https://github.com/chenxinfeng4/ArControl
Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.
Proper citation: ArControl (RRID:SCR_021605) Copy
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